The genome information files of Stellera chamaejasme

AbstractUnderstanding how populations diverge and new species arise is a central questionin evolutionary biology. “Allopatric” divergence through geographical isolation is con?sidered to be the commonest mechanism generating species biodiversity in mountainecosystems. However, the underlying genomic dynamics, especially genomic islandsof elevated divergence and genes that are highly diverged as a result of lineage?specific selection, remain poorly understood. <i>Stellera chamaejasme</i> has a wide geo?graphical range across the Qinghai–Tibet Plateau and northern China, making it agood model with which to explore genomic divergence during speciation in mountainecosystems. We assembled a high-quality, chromosome-level genome for this speciesand resequenced the genomes of 24 populations across its major distribution. Ourpopulation genomic analyses recovered four distinct genetic lineages correspond?ing to geographical distributions with contrasting environments. However, we re?vealed continuous gene flow during the historical divergences of these four lineages.Interlineage hybrids and plastome introgressions were frequently found in regions ofcontact, which further increased gene flow between two contacting lineages in therecent past. The elevated divergences were highly heterogeneous across the genomeand selection of ancestral polymorphisims and divergence hitchhiking contributedgreatly to the formation of genomic islands. The highly diverged and lineage-specificpositively selected genes within and outside genomic islands were annotated to bemainly involved in local adaptation. Our results suggest that genomic divergence in<i>S. chamaejasme</i> is likely to have been triggered and maintained by local selection to?gether with geographical isolation.

摘要 解析种群分化与新物种形成的机制，是进化生物学的核心研究议题。通过地理隔离实现的异域分化（Allopatric divergence），被认为是山地生态系统物种多样性产生的最普遍机制。然而，其背后的潜在基因组动态过程，尤其是分化程度升高的基因组岛（genomic islands）、以及由谱系特异性选择（lineage-specific selection）介导的高度分化基因，仍有待深入阐释。狼毒（*Stellera chamaejasme*）在青藏高原与中国北部拥有广泛的地理分布范围，是探索山地生态系统物种形成过程中基因组分化的理想研究模型。本研究为该物种组装了高质量染色体水平基因组（chromosome-level genome），并对其主要分布区内的24个种群开展了基因组重测序。群体基因组分析（population genomic analyses）结果显示，该物种可划分为4个独立的遗传谱系（genetic lineages），这些谱系与对应的地理分布及环境差异高度匹配。不过，研究揭示在这4个谱系的历史分化进程中，始终存在持续的基因流（gene flow）。在谱系接触区域内，谱系间杂交个体与质体基因组渐渗（plastome introgressions）现象频繁出现，这进一步提升了近代两个接触谱系间的基因交流水平。全基因组的分化程度呈现高度异质性，祖先多态性保留与分化搭车效应（divergence hitchhiking）对基因组岛的形成贡献显著。位于基因组岛内及岛外的高度分化、谱系特异性正选择基因（positively selected genes），主要被注释为参与本地适应（local adaptation）相关的生物学过程。本研究结果表明，狼毒的基因组分化，可能由地理隔离与本地选择共同驱动并维持。